I think there must be something a little wrong that machine. I just created 65536 files named "1" to "65536" in a folder to test this out.

I managed to move all the files beginning with "1" to a folder using the move command in about 40 seconds. I then moved 5000 files to another folder using Explorer in about 20 seconds.

Admittedly Explorer takes a while to respond when you first navigate to the folder, but I have seen Linux some GUI file managers behave just as slowly when faced with similar numbers of files.

P.S. in Windows 2000 the Explorer 5000 file move would have taken forever, thankfully they optmised something in Explorer in XP when moving large numbers of files.